Variant report

Variant	rs7956397
Chromosome Location	chr12:57608338-57608339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:57608097-57608409	GM12878	blood:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
2	RAD21	chr12:57608114-57608410	SK-N-SH_RA	brain:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
3	RAD21	chr12:57607996-57608431	ECC-1	luminal epithelium:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
4	CTCF	chr12:57608117-57608372	MCF-7	breast:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
5	CTCF	chr12:57608200-57608350	AG09319	gingival:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
6	ELF1	chr12:57607701-57608391	A549	lung:	n/a	chr12:57607977-57607990 chr12:57608309-57608321 chr12:57607790-57607801 chr12:57607979-57607990
7	SIN3A	chr12:57607980-57608419	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr12:57608099-57608368	Kidney_OC	kidney:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
9	CTCF	chr12:57608102-57608381	Pancreas_OC	pancreas:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
10	CTCF	chr12:57608200-57608350	GM12864	blood:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
11	CTCF	chr12:57608136-57608357	MCF-7	breast:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
12	GTF2F1	chr12:57607812-57608357	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:57606903-57610506	U87	brain:	n/a	n/a
14	CTBP2	chr12:57607083-57608538	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF12	chr12:57607124-57608551	ECC-1	luminal epithelium:	n/a	chr12:57608410-57608420 chr12:57607780-57607788 chr12:57607687-57607694
16	CTCF	chr12:57608060-57608638	GM19238	blood:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
17	RAD21	chr12:57608101-57608352	K562	blood:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
18	RAD21	chr12:57608109-57608429	HepG2	liver:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
19	CTCF	chr12:57608106-57608355	A549	lung:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
20	POLR2A	chr12:57607156-57608345	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:57607153-57610401	U87	brain:	n/a	n/a
22	CTCF	chr12:57608088-57608406	Spleen_OC	spleen:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
23	POLR2A	chr12:57608000-57608998	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr12:57607920-57608537	HCT-116	colon:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
25	RFX5	chr12:57608032-57608405	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr12:57608099-57608402	ECC-1	luminal epithelium:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
27	POLR2A	chr12:57607918-57608751	PFSK-1	brain:	n/a	n/a
28	CTCF	chr12:57608121-57608383	MCF-7	breast:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
29	RAD21	chr12:57607994-57608470	A549	lung:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
30	CTCF	chr12:57607994-57608450	K562	blood:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
31	MYC	chr12:57608082-57608490	H1-hESC	embryonic stem cell:	n/a	chr12:57608308-57608318
32	CTCF	chr12:57608133-57608365	ProgFib	skin:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
33	POLR2A	chr12:57608133-57608410	HepG2	liver:	n/a	n/a
34	CTCF	chr12:57608200-57608350	SK-N-SH_RA	brain:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
35	SMC3	chr12:57607908-57608806	SK-N-SH	brain:	n/a	chr12:57608637-57608647 chr12:57608633-57608647 chr12:57608253-57608267 chr12:57608253-57608260 chr12:57608636-57608644
36	SMC3	chr12:57608084-57608424	K562	blood:	n/a	chr12:57608253-57608267 chr12:57608253-57608260
37	CTCF	chr12:57608023-57608431	H1-hESC	embryonic stem cell:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
38	POLR2A	chr12:57607125-57608981	HepG2	liver:	n/a	n/a
39	RAD21	chr12:57608125-57608424	K562	blood:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
40	RAD21	chr12:57607972-57608501	MCF-7	breast:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
41	BCL3	chr12:57607082-57608396	A549	lung:	n/a	n/a
42	CTCF	chr12:57608220-57608370	NHEK	skin:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
43	SMC3	chr12:57608038-57608465	Hela-S3	cervix:	n/a	chr12:57608253-57608267 chr12:57608253-57608260
44	RAD21	chr12:57608021-57608466	SK-N-SH_RA	brain:	n/a	chr12:57608252-57608271 chr12:57608253-57608267 chr12:57608253-57608262
45	CTCF	chr12:57607763-57608443	HepG2	liver:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
46	MAZ	chr12:57607846-57608436	Hela-S3	cervix:	n/a	chr12:57608308-57608318
47	CTCF	chr12:57608200-57608350	HA-sp	spinal cord:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
48	CTCF	chr12:57608200-57608350	NHEK	skin:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
49	CTCF	chr12:57608124-57608387	MCF-7	breast:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268
50	CTCF	chr12:57608117-57608375	GM13977	blood:	n/a	chr12:57608254-57608263 chr12:57608251-57608269 chr12:57608252-57608268

No.	Distal block	Cell Line	Cell type
1	chr12:57480154..57482467-chr12:57605881..57608725,2	K562	blood:
2	chr12:57606014..57610025-chr12:57631623..57633806,36	MCF-7	breast:
3	chr12:57607877..57611743-chr12:57643490..57646687,3	K562	blood:
4	chr12:57606792..57609175-chr12:57630908..57633525,50	K562	blood:
5	chr12:57607441..57608995-chr12:57610521..57612256,2	MCF-7	breast:
6	chr12:57606818..57608471-chr12:57912067..57913671,2	K562	blood:
7	chr12:57588577..57592670-chr12:57606671..57608811,3	K562	blood:
8	chr12:57588577..57590373-chr12:57606431..57608754,2	K562	blood:
9	chr12:57595870..57598070-chr12:57607882..57609452,2	K562	blood:
10	chr12:57608303..57611284-chr12:57611816..57613934,2	MCF-7	breast:
11	chr12:57608166..57609235-chr12:57637200..57637869,4	MCF-7	breast:
12	chr12:57606546..57610160-chr12:57612220..57614034,3	K562	blood:
13	chr12:57606466..57609055-chr12:57636459..57638396,24	K562	blood:
14	chr12:57578786..57581016-chr12:57606054..57608817,2	MCF-7	breast:
15	chr12:57606205..57609184-chr12:57636393..57638193,29	MCF-7	breast:
16	chr12:57607241..57608791-chr12:57610365..57612075,2	K562	blood:

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000185633	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000182379	Chromatin interaction
ENSG00000185482	Chromatin interaction
ENSG00000166881	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs35492427	0.85[AFR][1000 genomes]
rs7487148	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57585800-57608600	Strong transcription	NHLF	lung
2	chr12:57603200-57610200	Weak transcription	Right Atrium	heart
3	chr12:57605800-57609400	Weak transcription	Lung	lung
4	chr12:57606000-57608400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:57606400-57610200	Weak transcription	Aorta	Aorta
6	chr12:57606600-57608400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57606600-57608600	Enhancers	Fetal Brain Male	brain
8	chr12:57606600-57608600	Enhancers	Left Ventricle	heart
9	chr12:57606800-57608400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:57606800-57608400	Enhancers	Placenta	Placenta
11	chr12:57606800-57608600	Enhancers	A549	lung
12	chr12:57606800-57609000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:57606800-57609400	Weak transcription	Gastric	stomach
14	chr12:57606800-57609600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr12:57606800-57609600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:57606800-57609600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:57606800-57609800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr12:57606800-57610200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
19	chr12:57606800-57610200	Enhancers	Pancreas	Pancrea
20	chr12:57607000-57609200	Weak transcription	Liver	Liver
21	chr12:57607000-57609800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:57607200-57608400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr12:57607200-57608400	Enhancers	Spleen	Spleen
24	chr12:57607200-57608600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:57607200-57608600	Bivalent Enhancer	Fetal Thymus	thymus
26	chr12:57607200-57608600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
27	chr12:57607200-57608800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
28	chr12:57607200-57609600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:57607200-57610000	Enhancers	Right Ventricle	heart
30	chr12:57607200-57610800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:57607400-57608400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:57607400-57608400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:57607400-57608400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr12:57607400-57608400	Flanking Active TSS	Hela-S3	cervix
35	chr12:57607400-57609200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:57607400-57609400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr12:57607400-57609600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr12:57607400-57609600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr12:57607400-57609600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
40	chr12:57607400-57609600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr12:57607400-57609800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr12:57607400-57609800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr12:57607400-57610200	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr12:57607600-57608400	Bivalent Enhancer	Colonic Mucosa	Colon
45	chr12:57607600-57608400	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr12:57607600-57608600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:57607600-57608600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
48	chr12:57607600-57608600	Weak transcription	NHDF-Ad	bronchial
49	chr12:57607600-57609800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
50	chr12:57607600-57610200	Weak transcription	Ovary	ovary

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